I just had this problem and figured out how to fix it. The issue for me was that inside of Fallout 4's Data > Scripts > Source > Base there was a second Base folder. I moved all the contents of the second folder into the first (there were only 284 repeated files) and then I deleted the second Base folder.
I don't know how this issue was created, but it is certainly causing issues because the Creation Engine is looking for Data > Scripts > Source > Base "[New Script]" and the engine is NOT looking for Source > Base > Base "[New Script]".
Hope this helps!